After defeating Phantom Zant, stand a few feet from Zant's Hand and use the clawshot to release the Sol. Quickly clawshot the Sol and throw it at the indention in the floor behind Zant's Hand awakens.
Throw the Sol at the indention in the floor and while it's rolling, stand on the top of the unrisen staircase. When the cutscene activates and the staircase rises, you can proceed to the solid platform and clawshot the Sol.
Head over the right from the entrance into the twilight realm and throw the Gale Boomerang to long jump to the right wing, and skip riding the platform.
As in the previous staircase raising timesaver, stand on the top of the unrisen staircase and throw the Sol at the indention in the floor. After the stair raising cutscene, climb onto the solid platform and clawshot the Sol.
Pull out the clawshot and walk towards the wall of Twilight, aiming the clawshot at the wall where the clawshot medallion is. As so as you target the clawshot medallion, clawshot to it.
After riding the floating platform to the Zant mask, kill it then jump of the ledge to death warp back to the main platform. You must walk and jump off the platform, not roll, so that the enemy dies before you death warp.
From the start of the battle, equip the iron boots and wait for the large Zant mask to emerge. Once it appears, use the Air Replenish Trick to refresh you air meter, and grapple Zant towards you. Once you have dealt him enough damage so he disappears. Once he has returned to the Zant mask, refresh your air meter once more. From here, swim to the center of the room and wait for the masks to arise, and refresh your air meter one last time. Finish him off and proceed with the battle. An optimal battle with Zant during his underwater phase would take 3 water bombs, but because of the randomness of the fight, it is highly possible that the battle will take more than 3 water bombs.